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Chromosome lost after merge with vcf-merge

Hi all,

I have merged a number of WGS VCF files generated from the standard GATK pipeline with vcf-merge function of VCFtools. The merged big VCF file shows that the chromosomes after 19 (e.g., Chrom20) lost. I guess one/some individual VCF files do(es) not have the lost chroms. Are there any possibilities?

Bests

vcf-merge
• 2,039 views • link
written by boymin2020 • boymin2020

1 answer

vcf-merge is outdated. Can you retry with bcftools merge ? Also please paste the commands that you have used.

• 1 views • link
written by Kevin Blighe Kevin Blighe

Thanks for your advice. bcftools merge works much faster and very well.

• 1 views • link
written by boymin2020 • boymin2020

So, the question is resolved?

• 1 views • link
written by Kevin Blighe Kevin Blighe

Great. I've moved my comment to an answer, to help others. To re-iterate: BCFtools should be used in place of VCFtools in the future.

• 1 views • link
written by Kevin Blighe Kevin Blighe

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